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FF:10832-111D4: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0101035
|fonse_cell_line=FF:0101035
|fonse_cell_line_closure=FF:0101035
|fonse_cell_line_closure=FF:0101035

Revision as of 17:28, 29 March 2012


Name:acute myeloid leukemia (FAB M4eo) cell line:EoL-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age33
cell typeeosinophil progenitor cell
cell lineEoL-1 cell
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.156
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.609
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13056

Jaspar motifP-value
MA0002.21.92405e-4
MA0003.10.963
MA0004.10.104
MA0006.10.201
MA0007.10.541
MA0009.10.296
MA0014.10.753
MA0017.10.0249
MA0018.20.032
MA0019.10.0352
MA0024.11.33005e-5
MA0025.10.343
MA0027.10.255
MA0028.10.00134
MA0029.10.71
MA0030.10.0176
MA0031.10.311
MA0035.20.209
MA0038.10.0946
MA0039.20.229
MA0040.10.292
MA0041.10.156
MA0042.10.723
MA0043.10.496
MA0046.10.127
MA0047.20.611
MA0048.10.212
MA0050.10.736
MA0051.10.183
MA0052.10.0798
MA0055.10.105
MA0057.10.755
MA0058.10.0664
MA0059.18.44664e-4
MA0060.10.0405
MA0061.10.432
MA0062.21.47953e-6
MA0065.20.0337
MA0066.10.536
MA0067.10.921
MA0068.10.0656
MA0069.10.202
MA0070.10.764
MA0071.10.0495
MA0072.10.164
MA0073.10.962
MA0074.10.544
MA0076.16.86913e-4
MA0077.10.691
MA0078.10.67
MA0079.20.0647
MA0080.26.24686e-10
MA0081.10.00134
MA0083.10.282
MA0084.10.96
MA0087.10.458
MA0088.10.00703
MA0090.16.23408e-4
MA0091.10.373
MA0092.10.284
MA0093.10.1
MA0099.20.00785
MA0100.14.74749e-4
MA0101.10.845
MA0102.20.351
MA0103.10.543
MA0104.25.86756e-4
MA0105.10.00149
MA0106.10.128
MA0107.10.201
MA0108.25.19232e-11
MA0111.10.145
MA0112.20.0414
MA0113.10.869
MA0114.10.0555
MA0115.10.028
MA0116.15.10772e-6
MA0117.10.82
MA0119.10.435
MA0122.10.9
MA0124.10.855
MA0125.10.678
MA0131.10.248
MA0135.10.0508
MA0136.11.28301e-15
MA0137.20.994
MA0138.20.955
MA0139.10.393
MA0140.10.258
MA0141.10.035
MA0142.10.076
MA0143.10.129
MA0144.10.88
MA0145.10.513
MA0146.10.192
MA0147.11.29571e-4
MA0148.10.745
MA0149.10.14
MA0150.10.732
MA0152.10.374
MA0153.10.0771
MA0154.10.00702
MA0155.10.712
MA0156.12.21716e-8
MA0157.10.827
MA0159.10.253
MA0160.10.145
MA0162.10.683
MA0163.18.53314e-16
MA0164.10.876
MA0258.10.0772
MA0259.10.0625



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs13056

Novel motifP-value
10.0177
100.0114
1000.197
1010.241
1020.776
1030.125
1040.691
1050.496
1060.809
1070.509
1080.792
1090.0448
110.0479
1100.115
1110.0813
1120.458
1130.804
1140.0973
1150.918
1160.305
1170.0389
1180.0386
1190.196
120.857
1200.237
1210.874
1220.761
1230.0104
1240.242
1250.467
1260.182
1270.106
1280.827
1290.352
130.0211
1300.991
1310.479
1320.804
1330.613
1340.99
1350.856
1360.648
1370.217
1380.923
1390.237
140.966
1400.434
1410.0612
1420.417
1430.547
1440.603
1450.722
1460.893
1470.281
1480.0839
1490.832
150.0882
1500.632
1510.793
1520.124
1530.968
1540.811
1550.0806
1560.866
1570.144
1580.994
1590.411
160.811
1600.14
1610.068
1620.916
1630.17
1640.215
1650.0735
1660.518
1670.101
1680.976
1690.227
170.648
180.506
190.575
20.521
200.373
210.0755
220.704
230.253
240.179
250.161
260.0568
270.609
280.843
290.0104
30.0286
300.0926
310.888
320.53
330.319
340.747
350.124
360.00894
370.296
380.337
390.586
40.224
400.203
410.738
420.13
430.405
440.0523
450.358
460.0514
470.0191
480.0424
490.158
50.511
500.849
510.663
520.301
530.509
540.726
550.795
560.95
570.0637
580.21
590.446
60.391
600.847
610.263
620.0788
630.355
640.145
650.877
660.159
670.646
680.818
690.213
70.155
700.381
710.0158
720.894
730.679
740.503
750.0265
760.261
770.864
780.0429
790.48
80.0723
800.469
810.166
820.464
830.464
840.673
850.524
860.633
870.451
880.941
890.954
90.669
900.024
910.393
920.36
930.934
940.237
950.0528
960.621
970.342
980.279
990.438



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs13056


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
1240 (leukemia)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8692 (myeloid leukemia)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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